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- PDB-3lgm: Crystal structure of reduced IsdI in complex with heme -

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Basic information

Entry
Database: PDB / ID: 3lgm
TitleCrystal structure of reduced IsdI in complex with heme
ComponentsHeme-degrading monooxygenase isdI
KeywordsOXIDOREDUCTASE / Dimeric alpha+beta barrel / Cytoplasm / Heme / Iron / Metal-binding / Monooxygenase
Function / homology
Function and homology information


heme oxygenase (staphylobilin-producing) / iron import into cell / heme oxygenase (decyclizing) activity / heme catabolic process / iron ion binding / heme binding / cytoplasm
Similarity search - Function
Heme oxygenase IsdG / : / ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Heme oxygenase (staphylobilin-producing) 2
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsUkpabi, G.N. / Murphy, M.E.P.
CitationJournal: Mol.Microbiol. / Year: 2010
Title: The IsdG-family of haem oxygenases degrades haem to a novel chromophore
Authors: Reniere, M.L. / Ukpabi, G.N. / Harry, S.R. / Stec, D.F. / Krull, R. / Wright, D.W. / Bachmann, B.O. / Murphy, M.E.P. / Skaar, E.P.
History
DepositionJan 20, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heme-degrading monooxygenase isdI
B: Heme-degrading monooxygenase isdI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2885
Polymers26,0312
Non-polymers1,2573
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-16 kcal/mol
Surface area12380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.040, 68.030, 70.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Heme-degrading monooxygenase isdI / IsdI / Iron-regulated surface determinant isdI / Iron-responsive surface determinant isdI / Heme oxygenase


Mass: 13015.394 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: N315 / Gene: IsdI / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3)
References: UniProt: Q7A827, heme oxygenase (biliverdin-producing)
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsMAGNESIUM ION 600 IS COORDINATED BY 6 WATERS 601-606.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.15 % / Mosaicity: 1.09 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% polyethylene glycol 3350, 0.2M MgCl2, 0.1M Bis-Tris buffer pH 5.5, and soaked in 50mM sodium dithionite for 10 minutes with a cryoprotectant of 10% ethylene glycol before freezing, VAPOR ...Details: 25% polyethylene glycol 3350, 0.2M MgCl2, 0.1M Bis-Tris buffer pH 5.5, and soaked in 50mM sodium dithionite for 10 minutes with a cryoprotectant of 10% ethylene glycol before freezing, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 8, 2008
Details: DCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing mirror.
RadiationMonochromator: double crystal monochromator (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.88→70.75 Å / Num. all: 23396 / Num. obs: 23396 / % possible obs: 99.8 % / Redundancy: 7 % / Rsym value: 0.094

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZDP

2zdp


Resolution: 1.88→44.87 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.244 / WRfactor Rwork: 0.201 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.858 / SU B: 3.222 / SU ML: 0.096 / SU R Cruickshank DPI: 0.151 / SU Rfree: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1195 5.1 %RANDOM
Rwork0.2 ---
all0.221 23423 --
obs0.203 23323 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.43 Å2 / Biso mean: 29.569 Å2 / Biso min: 16.41 Å2
Baniso -1Baniso -2Baniso -3
1--1.46 Å20 Å20 Å2
2---0.54 Å20 Å2
3---2.01 Å2
Refinement stepCycle: LAST / Resolution: 1.88→44.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1845 0 87 184 2116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221988
X-RAY DIFFRACTIONr_angle_refined_deg1.3482.0672712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7265220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60125.495111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50415351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.566159
X-RAY DIFFRACTIONr_chiral_restr0.0930.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021547
X-RAY DIFFRACTIONr_mcbond_it0.8111.51098
X-RAY DIFFRACTIONr_mcangle_it1.53421775
X-RAY DIFFRACTIONr_scbond_it2.1833890
X-RAY DIFFRACTIONr_scangle_it3.5074.5937
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 89 -
Rwork0.283 1626 -
all-1715 -
obs-1715 100 %

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